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SSD connecting at SATA 3Gbps instead of 6Gbps when hot-swapped

I'm having a problem that I am not sure how to even begin to troubleshoot. I want to determine which component is most at fault and/or easiest to fix.

I have a couple Plextor SSDs, model M3P and M5P, and they both exhibit the same issue. When I hot-swap them on my linux box, they are somehow limited to SATA 3Gbps speed. I determined this by doing a sequential read using fio, and only getting 250MB/s.

If I boot with either of the Plextor SSDs attached (instead of hot-swapping), then they do work at SATA 6Gbps speeds -- sequential reads of over 400MB/s. But if I then hot-swap the SSD out and back in, it reverts to SATA 3Gbps speeds.

I have a Windows 7 machine, Intel DH67GD motherboard with two Intel SATA 6Gbps ports, that can hot-swap the same Plextor SSDs and they work at SATA 6Gbps speeds.

Even more perplexing is that I have two other SSDs, a Samsung 830 and a Samsung 840 Pro, and both of those are able to hot-swap and work at SATA 6Gbps speeds on my linux box.

So I am not sure whether to point the finger at the linux SATA driver, at the Supermicro X9SCM-iiF motherboard (tried both BIOS 2.0 and 2.0a) that is in my linux box, or at the Plextor SSDs themselves. If I blame the Plextor SSDs, then it is tough to explain why they hot-swap fine on my Windows box, but if I blame the linux driver or SM motherboard, then it is tough to explain why the Samsung SSDs hot-swap fine on the linux box.

By the way, I am connecting the Plextor SSDs to one of the two SATA 6Gbps ports on the X9SCM-iiF motherboard. So it is not a matter of me using a 3Gbps SATA port (and besides, it works at 6Gbps on the same port if I boot with the SSD attached). Also, in the BIOS configuration, all of the SATA ports have hot-swap enabled.

Any suggestions on how to troubleshoot this? What linux commands might I try to investigate further?

Here is an example of the kernel log when I hotswap various SSDs. Note that the Plextor M5P connects incorrectly at 3.0 Gbps after the hard reset, but the Samsung 840 Pro connects at 6.0 Gbps after the hard reset.